Article
Physics, Fluids & Plasmas
Daniel Janosi, Tamas Tel
Summary: This paper proposes viable alternative approaches to characterize chaos in systems subjected to parameter drift. By following stable and unstable foliations, information about time-dependent chaos can be obtained. The characteristics of the foliations also vary in dissipative and Hamiltonian cases.
Article
Physics, Multidisciplinary
Yuanzhao Zhang, Steven H. Strogatz
Summary: The study reveals that the attractor basins formed by Kuramoto oscillators in high-dimensional dynamical systems exhibit octopus-like characteristics, with the majority of their volume located in the tentacles rather than the head region. This provides a simple geometric explanation for the common occurrence of basins with tentacles in high-dimensional systems.
PHYSICAL REVIEW LETTERS
(2021)
Article
Computer Science, Artificial Intelligence
Jiali Yu, Wenshuang Chen, Jinsong Leng, Chunxiao Wang, Zhang Yi
Summary: Continuous attractor refers to a low-dimensional manifold embedded in a high-dimensional state space. Line attractor is a one-dimensional continuous attractor, while plane attractor is a two-dimensional continuous attractor. The weight matrix and external input are crucial for expressing the continuous attractor. This paper provides conditions for parameter selection to achieve line attractor and plane attractor. The type and shape of the continuous attractor can be heavily affected even by a small perturbation of the parameters. The parameter selection scheme is crucial for designing neural network models.
Article
Engineering, Mechanical
Qiuzhen Wan, Simiao Chen, Qiao Yang, Jiong Liu, Kunliang Sun
Summary: This paper proposes a novel method for generating grid multi-scroll attractors based on a memristive Hopfield neural network. Theoretical analysis and numerical simulations reveal that the chaotic behavior of the network can be stabilized to periodic behavior by appropriate external pulse current stimulation. The introduction of a multi-piecewise memristor allows for the generation of various complex grid multi-scroll attractors. A physical circuit implementing the grid multi-scroll attractors is presented using basic commercial electronic components.
NONLINEAR DYNAMICS
(2023)
Article
Computer Science, Artificial Intelligence
Masaki Kobayashi
Summary: The paper introduces a synthetic Hopfield neural network (SHNN) that combines a complex-valued Hopfield neural network (CHNN) and a hyperbolic-valued Hopfield neural network (HHNN). CHNN and HHNN are represented by matrices and vectors to form SHNN, with the common global minima being the global minima of SHNN. Computer simulations support the improvement in noise tolerance expected from SHNN.
Article
Biotechnology & Applied Microbiology
Yongqing Zhang, Qingyuan Chen, Meiqin Gong, Yuanqi Zeng, Dongrui Gao
Summary: This study proposes constructing gene regulatory networks under different molecular subtypes of MIBC and analyzing the regulatory differences. Differential expression analysis and network analysis revealed significant differences in expression and regulatory relationships of genes such as SERPINI1, NOTUM, and FGFR1. Pathway enrichment analysis showed pathways like Neuroactive ligand-receptor interaction and Cytokine-cytokine receptor interaction are significantly enriched with diverse genes in bladder cancer subtypes.
Article
Oncology
Nirakar Rajbhandari, Michael Hamilton, Cynthia M. Quintero, L. Paige Ferguson, Raymond Fox, Christian M. Schuerch, Jun Wang, Mari Nakamura, Nikki K. Lytle, Matthew Mcdermott, Emily Diaz, Hannah Pettit, Marcie Kritzik, Haiyong Han, Derek Cridebring, Kwun Wah Wen, Susan Tsai, Michael G. Goggins, Andrew M. Lowy, Robert J. Wechsler-Reya, Daniel D. Von Hoff, Aaron M. Newman, Tannishtha Reya
Summary: Through single-cell genomics analysis, this study reveals that multiple pancreatic cancer subtypes can arise from a common pool of MSI2+ pancreatic cells, which establish different subtypes by activating distinct transcriptional programs and large-scale genomic changes.
Article
Automation & Control Systems
Xiaoqing Cheng, Wai-Ki Ching, Sini Guo, Tatsuya Akutsu
Summary: Observing the internal state of a whole system using a small number of sensor nodes is crucial in analysis of complex networks. This study addresses the problem of determining the minimum number of sensor nodes needed to discriminate attractors, presenting exact and approximation algorithms for this minimization problem. The effectiveness of the algorithms is demonstrated through computational experiments with both synthetic and realistic biological data.
Article
Mathematics, Interdisciplinary Applications
Miao Wang, Yuru Wang, Ran Chu
Summary: This article investigates the dynamical analysis of the incommensurate fractional-order neural network and provides insights for simulating complex neural system states in pathological conditions. The Adomian decomposition method algorithm is used to solve the incommensurate fractional-order Hopfield neural network system. Different dynamical behaviors of the system are explored and discussed by varying the order values. The results show complex and interesting phenomena, providing a theoretical basis for the later study of incommensurate fractional-order neural network systems.
FRACTAL AND FRACTIONAL
(2023)
Article
Oncology
Katherine Foster, Katelyn F. Handley, Deanna Glassman, Travis T. Sims, Sanaz Javadi, Sarah M. Palmquist, Mohammed M. Saleh, Bryan M. Fellman, Nicole D. Fleming, Priya R. Bhosale, Anil K. Sood
Summary: By analyzing CT scans and laparoscopic assessments of 109 patients with high-grade serous ovarian cancer, radiographic features unique to each morphologic subtype were identified, including large infiltrative plaques, mass-like metastases, and enhancing peritoneal lining. These findings provide valuable insights for the accurate diagnosis and classification of high-grade serous ovarian cancer.
INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER
(2023)
Article
Multidisciplinary Sciences
Yuanxiang Jiang, Meng Li, Ying Fan, Zengru Di
Summary: Measuring the dissimilarities between networks is a fundamental problem widely used in various fields. This study proposes a quantitative dissimilarity metric for weighted networks (WD-metric) based on the D-measure method, which can effectively capture the influence of weight on network structure. Experimental results demonstrate the effectiveness of WD-metric and its potential as a criterion for backbone extraction algorithms in complex networks.
SCIENTIFIC REPORTS
(2021)
Article
Computer Science, Artificial Intelligence
Han Bao, Richong Zhang, Yongyi Mao
Summary: This paper revisits the capacity of dense associative memory (DAM) networks and presents a capacity theorem with an attraction radius or noise level. It demonstrates that probes can converge to targeted messages after one-step updates, and the capacity of DAM networks falls within a range between lower and upper bounds. The study also explores a more general notion of capacity allowing retrieval from noisy probes, providing theoretical proofs and simulated experiments for validation.
Article
Computer Science, Software Engineering
Ludwig Kampel, Michael Wagner, Ilias S. Kotsireas, Dimitris E. Simos
Summary: In this study, neural networks in the form of Boltzmann machines and Hopfield networks are used to construct a specific class of combinatorial designs called covering arrays. By adapting existing algorithms and conducting comprehensive experimental evaluations, the research demonstrates the first application of neural networks in the field of covering array generation and related discrete structures.
OPTIMIZATION METHODS & SOFTWARE
(2022)
Article
Chemistry, Multidisciplinary
Fiona Mukherjee, Anye Shi, Xin Wang, Fengqi You, Nicholas L. Abbott
Summary: This study explores the formation of distinct 2D patterns of microplastics (MPs) at the aqueous interfaces of liquid crystal (LC) films, aiming to develop surface-sensitive methods for identifying MPs. Polyethylene (PE) and polystyrene (PS) microparticles exhibit different aggregation patterns, with anionic surfactant amplifying the differences in aggregation patterns. Statistical analysis using deep learning image recognition models accurately classifies the assembly patterns, with dense, multibranched assemblies identified as unique features of PE. The study predicts LC-mediated interactions and concludes that rough surfaces of PE microparticles weaken LC elastic interactions and enhance capillary forces. Overall, LC interfaces show potential for rapid identification of colloidal MPs based on their surface properties.
Article
Mathematics, Applied
Fabio Schittler Neves, Marc Timme
Summary: This research proposes an efficient decoding scheme for trajectories in spiking neural circuits which exhibit linear scaling with input signal dimensionality, overcoming challenges related to high-dimensional state-space decoding. By identifying simple measures of coordinated activity and designing robust readouts, efficient decoding strategies in spiking neural networks can be catalyzed with linear increase in sizes and time requirements.
Article
Biology
Harald Oey, Martha Zakrzewski, Kanwar Narain, K. Rekha Devi, Takeshi Agatsuma, Sujeevi Nawaratna, Geoffrey N. Gobert, Malcolm K. Jones, Mark A. Ragan, Donald P. McManus, Lutz Krause
Article
Microbiology
Harald Oey, Martha Zakrzewski, Kerstin Gravermann, Neil D. Young, Pasi K. Korhonen, Geoffrey N. Gobert, Sujeevi Nawaratna, Shihab Hasan, David M. Martinez, Hong You, Martin Lavin, Malcolm K. Jones, Mark A. Ragan, Jens Stoye, Ana Oleaga, Aidan M. Emery, Bonnie Webster, David Rollinson, Robin B. Gasser, Donald P. McManus, Lutz Krause
Article
Oncology
K. Nones, J. Johnson, F. Newell, A. M. Patch, H. Thorne, S. H. Kazakoff, X. M. de Luca, M. T. Parsons, K. Ferguson, L. E. Reid, A. E. McCart Reed, S. Srihari, V Lakis, A. L. Davidson, P. Mukhopadhyay, O. Holmes, Q. Xu, S. Wood, C. Leonard, J. Beesley, J. M. Harris, D. Barnes, A. Degasperi, M. A. Ragan, A. B. Spurdle, K. K. Khanna, S. R. Lakhani, J. Pearson, S. Nik-Zainal, G. Chenevix-Trench, N. Waddell, P. T. Simpson
ANNALS OF ONCOLOGY
(2019)
Review
Ecology
Raul A. Gonzalez-Pech, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
TRENDS IN ECOLOGY & EVOLUTION
(2019)
Review
Zoology
Cornelia Jaspers, Sebastian Fraune, A. Elizabeth Arnold, David J. Miller, Thomas C. G. Bosch, Christian R. Voolstra, Maja Adamska, Tracy Ainsworth, Eldon Ball, Chloe Boote, David Bourne, Nicholas J. Butterfield, Cheong Xin Chan, Ira Cooke, Peter F. Cowman, Aaron Darling, Simon K. Davy, Amin Mohamed, Katharina Fabricius, Sofia Fortunato, Alejandra Hernandez, Mia Hoogenboom, Aurelie Moya, Lucia Pita, Mark A. Ragan, Steven J. Robbins, Natalia R. Andrade, Kazuhiro Sakamaki, Verena Schoepf, Thorsten Seemann, Chuya Shinzato, Jaroslaw Stolarski, Jan Strugnell, Shunichi Takahashi, Sen-Lin Tang, Nicole Webster, Brooke Whitelaw, Hua Ying
Review
Zoology
Ira Cooke, Oliver Mead, Casey Whalen, Chloe Boote, Aurelie Moya, Hua Ying, Steven Robbins, Jan M. Strugnell, Aaron Darling, David Miller, Christian R. Voolstra, Maja Adamska, Tracy Ainsworth, Natalia R. Andrade, A. Elizabeth Arnold, Eldon Ball, David Bourne, Thomas C. G. Bosch, Nicholas J. Butterfield, Cheong Xin Chan, Peter F. Cowman, Simon K. Davy, Katharina Fabricius, Sofia Fortunato, Sebastian Fraune, Alejandra Hernandez, Mia Hoogenboom, Cornelia Jaspers, Amin Mohamed, Lucia Pita, Mark A. Ragan, Kazuhiro Sakamaki, Verena Schoepf, Torsten Seemann, Chuya Shinzato, Jaroslaw Stolarski, Shunichi Takahashi, Sen-Lin Tang, Nicole Webster, Brooke Whitelaw
Article
Microbiology
Steven J. Robbins, Caitlin M. Singleton, Cheong Xin Chan, Lauren F. Messer, Aileen U. Geers, Hua Ying, Alexander Baker, Sara C. Bell, Kathleen M. Morrow, Mark A. Ragan, David J. Miller, Sylvain Foret, Christian R. Voolstra, Gene W. Tyson, David G. Bourne, Eldon Ball, Roger Beeden, Michael Berumen, Manuel Aranda, Timothy Ravasi, Pim Bongaerts, Ove Hoegh-Guldberg, Ira Cooke, Bill Leggat, Susan Sprungala, Anna Fitzgerald, Catherine Shang, Petra Lundgren, Theresa Fyffe, Francesco Rubino, Madeleine van Oppen, Karen Weynberg, Sara C. Bells
NATURE MICROBIOLOGY
(2019)
Article
Biology
Timothy G. Stephens, Raul A. Gonzalez-Pech, Yuanyuan Cheng, Amin Mohamed, David W. Burt, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
Article
Environmental Sciences
Amin R. Mohamed, Cheong Xin Chan, Mark A. Ragan, Jia Zhang, Ira Cooke, Eldon E. Ball, David J. Miller
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2020)
Article
Biology
Raul A. Gonzalez-Pech, Timothy G. Stephens, Yibi Chen, Amin R. Mohamed, Yuanyuan Cheng, Sarah Shah, Katherine E. Dougan, Michael D. A. Fortuin, Remi Lagorce, David W. Burt, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
Summary: Genome sequences of Symbiodiniaceae are still scarce due to their large genome sizes and unique genome features. This study presented de novo genome assemblies of seven members of the genus Symbiodinium, revealing high sequence and structural divergence among different lineages, with some Symbiodinium isolates showing comparable divergence to distinct genera of Symbiodiniaceae.
Article
Biochemistry & Molecular Biology
Pim Bongaerts, Ira R. Cooke, Hua Ying, Dagmar Wels, Stijn den Haan, Alejandra Hernandez-Agreda, Christopher A. Brunner, Sophie Dove, Norbert Englebert, Gal Eyal, Sylvain Foret, Mila Grinblat, Kyra B. Hay, Saki Harii, David C. Hayward, Yu Lin, Mihaljevi C. Morana, Aurelie Moya, Paul Muir, Frederic Sinniger, Patrick Smallhorn-West, Gergely Torda, Mark A. Ragan, Madeleine J. H. van Oppen, Ove Hoegh-Guldberg
Summary: DNA sequencing studies are challenging the notion that the diversity of coral species is accurately described. Research has found that coral species can have ecological and phenotypic differences even if they are morphologically similar. This discovery highlights the potential role of temporal reproductive isolation in driving ecological and phenotypic divergence in coral species.
Review
Biochemistry & Molecular Biology
Katherine E. Dougan, Raul A. Gonzalez-Pech, Timothy G. Stephens, Sarah Shah, Yibi Chen, Mark A. Ragan, Debashish Bhattacharya, Cheong Xin Chan
Summary: Modern microbial taxonomy often relies on single or concatenated marker genes for classification. However, using whole-genome data can provide more accurate classification, especially for microbial eukaryotes.
TRENDS IN MICROBIOLOGY
(2022)
Meeting Abstract
Plant Sciences
Katherine E. Dougan, Raul A. Gonzalez-Pech, Timothy G. Stephens, Sarah Shah, Yibi Chen, Mark A. Ragan, Debashish Bhattacharya, Cheong Xin Chan
Article
Multidisciplinary Sciences
Ira Cooke, Hua Ying, Sylvain Foret, Pim Bongaerts, Jan M. Strugnell, Oleg Simakov, Jia Zhang, Matt A. Field, Mauricio Rodriguez-Lanetty, Sara C. Bell, David G. Bourne, Madeleine J. H. van Oppen, Mark A. Ragan, David J. Miller
Article
Biochemical Research Methods
Guillaume Bernard, Cheong Xin Chan, Yao-ban Chan, Xin-Yi Chua, Yingnan Cong, James M. Hogan, Stefan R. Maetschke, Mark A. Ragan
BRIEFINGS IN BIOINFORMATICS
(2019)